From 76f6f917b874d843f1dcbe76b1246a47e1ca165a Mon Sep 17 00:00:00 2001
From: Tasnim Mehzabin <tasnim.mehzabin@live.com>
Date: Wed, 31 Jul 2024 16:24:09 +0200
Subject: [PATCH] feat: add BAO Ontology terms (#1961)

---
 app/packs/src/apps/admin/AdminHome.js      |     2 +-
 app/packs/src/apps/admin/OlsTerms.js       |     5 +-
 public/ontologies_default/bao.default.json | 13542 +++++++++++++++++++
 3 files changed, 13547 insertions(+), 2 deletions(-)
 create mode 100644 public/ontologies_default/bao.default.json

diff --git a/app/packs/src/apps/admin/AdminHome.js b/app/packs/src/apps/admin/AdminHome.js
index f4180fa1d4..b347151aaf 100644
--- a/app/packs/src/apps/admin/AdminHome.js
+++ b/app/packs/src/apps/admin/AdminHome.js
@@ -86,7 +86,7 @@ class AdminHome extends React.Component {
             <NavItem eventKey={7}>UI features</NavItem>
             <NavItem eventKey={8}>Text Templates</NavItem>
             <NavItem eventKey={2}>Message Publish</NavItem>
-            <NavItem eventKey={5}>Load OLS Terms</NavItem>
+            <NavItem eventKey={5}>Load Ontology Terms</NavItem>
             {/* <NavItem eventKey={12}>Report-template Management</NavItem> */}
             <NavItem eventKey={13}>Delayed Jobs </NavItem>
             <NavItem eventKey={14}>ChemSpectra Layouts </NavItem>
diff --git a/app/packs/src/apps/admin/OlsTerms.js b/app/packs/src/apps/admin/OlsTerms.js
index dbf0b75638..4a919bced5 100644
--- a/app/packs/src/apps/admin/OlsTerms.js
+++ b/app/packs/src/apps/admin/OlsTerms.js
@@ -166,7 +166,7 @@ export default class OlsTerms extends React.Component {
         <Row style={{ maxWidth: '2000px', maxHeight: '1000px', margin: 'auto' }}>
           {this.dropzoneOrfilePreview()}
           <ButtonToolbar>
-            <Button bsStyle="warning" onClick={() => this.handleClick()}>Import OLS Terms (the file name will be the OLS_name)</Button>
+            <Button bsStyle="warning" onClick={() => this.handleClick()}>Import Ontology Terms (the file name will be the OLS_name)</Button>
           </ButtonToolbar>
         </Row>
         <Row style={{ maxWidth: '2000px', maxHeight: '1000px', margin: 'auto' }}>
@@ -178,6 +178,9 @@ export default class OlsTerms extends React.Component {
               <MenuItem key="chmo" onSelect={() => this.handleSelectName('chmo')}>
                 chmo
               </MenuItem>
+              <MenuItem key="chmo" onSelect={() => this.handleSelectName('bao')}>
+                bao
+              </MenuItem>
             </DropdownButton>
             <div><h3>{this.state.selectName}</h3></div>
             <Button
diff --git a/public/ontologies_default/bao.default.json b/public/ontologies_default/bao.default.json
new file mode 100644
index 0000000000..3d8548166c
--- /dev/null
+++ b/public/ontologies_default/bao.default.json
@@ -0,0 +1,13542 @@
+{
+    "ols_terms": [{
+            "title": "-- Recently selected --",
+            "value": "-- Recently selected --",
+            "selectable": false,
+            "children": []
+        }, {
+            "term_id": null,
+            "synonyms": null,
+            "synonym": null,
+            "search": "BAO:0002753 | assay method component",
+            "title": "assay method component",
+            "value": "BAO:0002753 | assay method component $1245c6b5-33a1-4f93-97e7-b018d0131e9a",
+            "is_enabled": true,
+            "id": "0002753",
+            "children": [{
+                    "term_id": null,
+                    "synonyms": null,
+                    "synonym": null,
+                    "search": "BAO:0000035 | physical detection method",
+                    "title": "physical detection method",
+                    "value": "BAO:0000035 | physical detection method $7308161b-c30d-4087-a2c4-3b55793bf953",
+                    "is_enabled": true,
+                    "id": "0000035",
+                    "children": [{
+                            "term_id": null,
+                            "synonyms": null,
+                            "synonym": null,
+                            "search": "BAO:0000046 | fluorescence method",
+                            "title": "fluorescence method",
+                            "value": "BAO:0000046 | fluorescence method $6916710f-2de6-4a02-9268-0555e0326a4b",
+                            "is_enabled": true,
+                            "id": "0000046",
+                            "children": [{
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000003 | fluorescence polarization",
+                                    "title": "fluorescence polarization",
+                                    "value": "BAO:0000003 | fluorescence polarization $ed42c354-92b9-4d99-b539-f452ec2fd9a5",
+                                    "is_enabled": true,
+                                    "id": "0000003",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000005 | flow cytometry",
+                                    "title": "flow cytometry",
+                                    "value": "BAO:0000005 | flow cytometry $9219079e-9221-4971-9118-dd1445267c75",
+                                    "is_enabled": true,
+                                    "id": "0000005",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000001 | fluorescence resonance energy transfer",
+                                    "title": "fluorescence resonance energy transfer",
+                                    "value": "BAO:0000001 | fluorescence resonance energy transfer $7e9db54f-5c8c-4370-b352-b1828c4eca10",
+                                    "is_enabled": true,
+                                    "id": "0000001",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000002 | homogeneous time resolved fluorescence",
+                                            "title": "homogeneous time resolved fluorescence",
+                                            "value": "BAO:0000002 | homogeneous time resolved fluorescence $a4fe0853-cb37-42e4-ae98-fef3d44407aa",
+                                            "is_enabled": true,
+                                            "id": "0000002",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000004 | time resolved fluorescence resonance energy transfer",
+                                            "title": "time resolved fluorescence resonance energy transfer",
+                                            "value": "BAO:0000004 | time resolved fluorescence resonance energy transfer $b44500f3-6c6d-4cdf-91be-d4642e7f5042",
+                                            "is_enabled": true,
+                                            "id": "0000004",
+                                            "children": []
+                                        }
+                                    ]
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000058 | thermal shift",
+                                    "title": "thermal shift",
+                                    "value": "BAO:0000058 | thermal shift $5ef96073-ef08-47c2-8a7a-d9ac2ae94ccb",
+                                    "is_enabled": true,
+                                    "id": "0000058",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000363 | fluorescence intensity",
+                                    "title": "fluorescence intensity",
+                                    "value": "BAO:0000363 | fluorescence intensity $1e33b507-ae07-470f-a105-23bbe0dd5bf7",
+                                    "is_enabled": true,
+                                    "id": "0000363",
+                                    "children": []
+                                }
+                            ]
+                        }, {
+                            "term_id": null,
+                            "synonyms": null,
+                            "synonym": null,
+                            "search": "BAO:0000049 | spectrophotometry method",
+                            "title": "spectrophotometry method",
+                            "value": "BAO:0000049 | spectrophotometry method $d2310380-6f7f-4707-a354-f07f2bb00065",
+                            "is_enabled": true,
+                            "id": "0000049",
+                            "children": [{
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0002529 | atomic absorption spectrophotometry",
+                                    "title": "atomic absorption spectrophotometry",
+                                    "value": "BAO:0002529 | atomic absorption spectrophotometry $b38c4787-974b-4e67-982a-5100202dd928",
+                                    "is_enabled": true,
+                                    "id": "0002529",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000071 | transmittance",
+                                    "title": "transmittance",
+                                    "value": "BAO:0000071 | transmittance $ea3901e3-8044-4d21-a9f3-51c7650cf81f",
+                                    "is_enabled": true,
+                                    "id": "0000071",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000070 | absorbance",
+                                    "title": "absorbance",
+                                    "value": "BAO:0000070 | absorbance $452877ae-678c-4018-be1d-0ce0f6050100",
+                                    "is_enabled": true,
+                                    "id": "0000070",
+                                    "children": []
+                                }
+                            ]
+                        }, {
+                            "term_id": null,
+                            "synonyms": null,
+                            "synonym": null,
+                            "search": "BAO:0000045 | luminescence method",
+                            "title": "luminescence method",
+                            "value": "BAO:0000045 | luminescence method $1518414b-40a4-4293-be16-ed8b088e3808",
+                            "is_enabled": true,
+                            "id": "0000045",
+                            "children": [{
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000130 | alphascreen",
+                                    "title": "alphascreen",
+                                    "value": "BAO:0000130 | alphascreen $121add39-6659-431f-b55a-d078a2a24b6e",
+                                    "is_enabled": true,
+                                    "id": "0000130",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000050 | bioluminescence",
+                                    "title": "bioluminescence",
+                                    "value": "BAO:0000050 | bioluminescence $b3017bfd-5e4d-4793-a041-b47804c36d8a",
+                                    "is_enabled": true,
+                                    "id": "0000050",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000461 | bioluminescence resonance energy transfer",
+                                            "title": "bioluminescence resonance energy transfer",
+                                            "value": "BAO:0000461 | bioluminescence resonance energy transfer $fbdbe037-fb07-4025-950d-04ce04ccde58",
+                                            "is_enabled": true,
+                                            "id": "0000461",
+                                            "children": []
+                                        }
+                                    ]
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000051 | chemiluminescence",
+                                    "title": "chemiluminescence",
+                                    "value": "BAO:0000051 | chemiluminescence $e6187d54-958d-48dc-b104-b0221a565318",
+                                    "is_enabled": true,
+                                    "id": "0000051",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000462 | chemiluminescence resonance energy transfer",
+                                            "title": "chemiluminescence resonance energy transfer",
+                                            "value": "BAO:0000462 | chemiluminescence resonance energy transfer $41fe403e-b52f-4ba2-81e8-37c38d7d56f5",
+                                            "is_enabled": true,
+                                            "id": "0000462",
+                                            "children": []
+                                        }
+                                    ]
+                                }
+                            ]
+                        }, {
+                            "term_id": null,
+                            "synonyms": null,
+                            "synonym": null,
+                            "search": "BAO:0000055 | mass spectrometry",
+                            "title": "mass spectrometry",
+                            "value": "BAO:0000055 | mass spectrometry $167204a3-a862-451a-8fa2-f79460f8b471",
+                            "is_enabled": true,
+                            "id": "0000055",
+                            "children": []
+                        }, {
+                            "term_id": null,
+                            "synonyms": null,
+                            "synonym": null,
+                            "search": "BAO:0000657 | radiometry method",
+                            "title": "radiometry method",
+                            "value": "BAO:0000657 | radiometry method $737187b1-44fe-4d98-a186-afd2d28b4763",
+                            "is_enabled": true,
+                            "id": "0000657",
+                            "children": [{
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0002527 | autoradiography",
+                                    "title": "autoradiography",
+                                    "value": "BAO:0002527 | autoradiography $db6857c5-424e-45df-8bca-c77797312ccd",
+                                    "is_enabled": true,
+                                    "id": "0002527",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "NCIT:C18639 | Quantitative Autoradiography",
+                                            "title": "Quantitative Autoradiography",
+                                            "value": "NCIT:C18639 | Quantitative Autoradiography $0aa93231-f00e-4ab9-b06f-0a5d65830cc7",
+                                            "is_enabled": true,
+                                            "id": "C18639",
+                                            "children": []
+                                        }
+                                    ]
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0002528 | phosphorimaging",
+                                    "title": "phosphorimaging",
+                                    "value": "BAO:0002528 | phosphorimaging $247b05bc-4c84-4635-8e80-5c28b225be81",
+                                    "is_enabled": true,
+                                    "id": "0002528",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000405 | scintillation counting",
+                                    "title": "scintillation counting",
+                                    "value": "BAO:0000405 | scintillation counting $6c1169f2-4ec9-44af-9489-3cf4db2ca2e7",
+                                    "is_enabled": true,
+                                    "id": "0000405",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000017 | scintillation proximity assay",
+                                            "title": "scintillation proximity assay",
+                                            "value": "BAO:0000017 | scintillation proximity assay $8d47df6f-36ab-492b-8da8-27084f41dbd8",
+                                            "is_enabled": true,
+                                            "id": "0000017",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000408 | lysate based",
+                                            "title": "lysate based",
+                                            "value": "BAO:0000408 | lysate based $11a9b85c-0410-4085-89ea-6f17fe46d814",
+                                            "is_enabled": true,
+                                            "id": "0000408",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000401 | filter assay",
+                                            "title": "filter assay",
+                                            "value": "BAO:0000401 | filter assay $27457ce2-cb9e-496c-b8b7-1dd93a5e533b",
+                                            "is_enabled": true,
+                                            "id": "0000401",
+                                            "children": []
+                                        }
+                                    ]
+                                }
+                            ]
+                        }, {
+                            "term_id": null,
+                            "synonyms": null,
+                            "synonym": null,
+                            "search": "BAO:0000427 | label free method",
+                            "title": "label free method",
+                            "value": "BAO:0000427 | label free method $aa8c9217-719e-413f-bffd-e38b9befd8ab",
+                            "is_enabled": true,
+                            "id": "0000427",
+                            "children": [{
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000160 | nuclear magnetic resonance",
+                                    "title": "nuclear magnetic resonance",
+                                    "value": "BAO:0000160 | nuclear magnetic resonance $8e95e22b-d6b1-4494-9b83-ed7e4fdc8917",
+                                    "is_enabled": true,
+                                    "id": "0000160",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000161 | circular dichroism",
+                                    "title": "circular dichroism",
+                                    "value": "BAO:0000161 | circular dichroism $0b9844c1-f156-451b-975e-f853ac1028b3",
+                                    "is_enabled": true,
+                                    "id": "0000161",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000163 | electrical sensor",
+                                    "title": "electrical sensor",
+                                    "value": "BAO:0000163 | electrical sensor $ee18c71e-5490-473b-829f-764f322a501d",
+                                    "is_enabled": true,
+                                    "id": "0000163",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000061 | impedance",
+                                            "title": "impedance",
+                                            "value": "BAO:0000061 | impedance $d56538f9-958b-4b92-b07d-adee50f8d25c",
+                                            "is_enabled": true,
+                                            "id": "0000061",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000382 | microelectrode measurement",
+                                            "title": "microelectrode measurement",
+                                            "value": "BAO:0000382 | microelectrode measurement $9400203c-72ac-4f0b-8619-eb47f0a9ec0b",
+                                            "is_enabled": true,
+                                            "id": "0000382",
+                                            "children": [{
+                                                    "term_id": null,
+                                                    "synonyms": null,
+                                                    "synonym": null,
+                                                    "search": "BAO:0000060 | current clamp",
+                                                    "title": "current clamp",
+                                                    "value": "BAO:0000060 | current clamp $1e659a1f-e429-4650-b010-50e93a983988",
+                                                    "is_enabled": true,
+                                                    "id": "0000060",
+                                                    "children": []
+                                                }, {
+                                                    "term_id": null,
+                                                    "synonyms": null,
+                                                    "synonym": null,
+                                                    "search": "BAO:0000063 | voltage clamp",
+                                                    "title": "voltage clamp",
+                                                    "value": "BAO:0000063 | voltage clamp $fb6c5e66-9077-4c9c-a7d7-811a8c3d0041",
+                                                    "is_enabled": true,
+                                                    "id": "0000063",
+                                                    "children": []
+                                                }, {
+                                                    "term_id": null,
+                                                    "synonyms": null,
+                                                    "synonym": null,
+                                                    "search": "BAO:0000062 | patch clamp",
+                                                    "title": "patch clamp",
+                                                    "value": "BAO:0000062 | patch clamp $3090eced-deed-4ed6-b0b2-a6f7c3918132",
+                                                    "is_enabled": true,
+                                                    "id": "0000062",
+                                                    "children": []
+                                                }
+                                            ]
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000471 | carbon nanotube based sensor",
+                                            "title": "carbon nanotube based sensor",
+                                            "value": "BAO:0000471 | carbon nanotube based sensor $67f729a4-277b-4e64-96b2-285bdf39b1bc",
+                                            "is_enabled": true,
+                                            "id": "0000471",
+                                            "children": []
+                                        }
+                                    ]
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000057 | optical based",
+                                    "title": "optical based",
+                                    "value": "BAO:0000057 | optical based $f0f44a4f-b119-4d68-9858-a2939100ce7c",
+                                    "is_enabled": true,
+                                    "id": "0000057",
+                                    "children": [{
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000069 | resonant waveguide grating",
+                                            "title": "resonant waveguide grating",
+                                            "value": "BAO:0000069 | resonant waveguide grating $b6d6ace9-8470-4c52-b6b2-95fa0aaf3ac6",
+                                            "is_enabled": true,
+                                            "id": "0000069",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000068 | optical waveguide grating",
+                                            "title": "optical waveguide grating",
+                                            "value": "BAO:0000068 | optical waveguide grating $6c7a0e4d-f938-412f-90b8-212937fd6ce0",
+                                            "is_enabled": true,
+                                            "id": "0000068",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000067 | fiber optic waveguide",
+                                            "title": "fiber optic waveguide",
+                                            "value": "BAO:0000067 | fiber optic waveguide $0ab20dc0-2eb1-4337-a9b1-4c48a117469d",
+                                            "is_enabled": true,
+                                            "id": "0000067",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000066 | bio layer interferometry",
+                                            "title": "bio layer interferometry",
+                                            "value": "BAO:0000066 | bio layer interferometry $493af6e9-3d5f-4f17-b3a3-91e177fbbaf6",
+                                            "is_enabled": true,
+                                            "id": "0000066",
+                                            "children": []
+                                        }, {
+                                            "term_id": null,
+                                            "synonyms": null,
+                                            "synonym": null,
+                                            "search": "BAO:0000054 | surface plasmon resonance",
+                                            "title": "surface plasmon resonance",
+                                            "value": "BAO:0000054 | surface plasmon resonance $0c18f6ad-63cf-42bd-8810-6be0470decaa",
+                                            "is_enabled": true,
+                                            "id": "0000054",
+                                            "children": []
+                                        }
+                                    ]
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
+                                    "synonym": null,
+                                    "search": "BAO:0000404 | x ray crystallography",
+                                    "title": "x ray crystallography",
+                                    "value": "BAO:0000404 | x ray crystallography $75768a8d-aa61-43c9-a48d-9a3aa4a72d9f",
+                                    "is_enabled": true,
+                                    "id": "0000404",
+                                    "children": []
+                                }, {
+                                    "term_id": null,
+                                    "synonyms": null,
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